Our results indicate that gene loops act to
maintain the directionality of transcription. The
loss of a mammalian gene’s PAS can directly
influence the recruitment of transcription factors, with a consequent reduction in gene expression (22). PAS mutation has also been shown to
increase levels of divergent transcripts (23). On
the basis of our results, such effects are directly
explicable by the loss of gene-loop formation and
the potential to recycle factors from the terminator back to the promoter (see model, Fig. 4D).
The role of Rpd3S in restricting antisense terminator transcripts (Fig. 3) clearly illustrates the
importance of histone deacetylation in preventing
inappropriate ncRNA synthesis. We predict that
gene loops may similarly act to influence the recruitment of 5′ localized histone deacetylases
such as Set3 (24). This would maintain promoters in a deacetylated, inactive state until gene activation selectively promotes transcription of genes
rather than divergent pSRTs. We postulate that
gene looping contributes to determining which
transcription units are fully productive.

Acknowledgments: We thank B. Dichtl and J. Kufel forstrains and H. Wijayatilake for FMP27 and b-globin 3Creagents. This work was supported by the Wellcome Trust(N.J.P.), the NIH and Deutsche Forschungsgemeinschaft(L.M.S.), European Molecular Biology Laboratory (J.B.Z.,N.M.L., L.M.S.), and the Swiss National Fonds and EuropeanMolecular Biology Organization (J.C.). Genomic data aredeposited at http://steinmetzlab.embl.de/proudfoot_lab/ index.html (E-TABM-936).

John R. Taylor1 and Roman Stocker2*Bacteria play an indispensable role in marine biogeochemistry by recycling dissolved organicmatter. Motile species can exploit small, ephemeral solute patches through chemotaxis and therebygain a fitness advantage over nonmotile competitors. This competition occurs in a turbulentenvironment, yet turbulence is generally considered inconsequential for bacterial uptake. Incontrast, we show that turbulence affects uptake by stirring nutrient patches into networks ofthin filaments that motile bacteria can readily exploit. We find that chemotactic motility is subjectto a trade-off between the uptake benefit due to chemotaxis and the cost of locomotion, resultingin an optimal swimming speed. A second trade-off results from the competing effects of stirringand mixing and leads to the prediction that chemotaxis is optimally favored at intermediateturbulence intensities.

The average milliliter of seawater contains a million heterotrophic bacteria that play an essential role in remineralizing dissolved
organic matter (DOM) by decomposing 35 to
80% of net primary production (1) and converting
it into particulate form, available for consumption
by larger organisms. Most marine environments
are turbulent, ranging from the energetic mixed-layer and surf zone to calmer thermoclines, yet
the effect of turbulence on bacterial uptake of
DOM has remained elusive. This is due in part
to the difficulty of quantifying the microscale
biogeochemical variability generated by turbu-

lence. At the same time, the physics of transport
at micrometer scales dictates that DOM uptake
occurs primarily by diffusion of nutrient molecules to cells (2). In a homogeneous nutrient
environment, marine turbulence is insufficient to
increase bacterial uptake (2, 3), at least for low–
molecular weight substrates. For example, relatively strong turbulence (D = 10−6 W kg−1, where
D is the turbulent dissipation rate) increases the
uptake of amino acids by <1%, and as a result
turbulence has been considered inconsequential
for bacterial uptake (2).